|
|
treatment
|
dataset_anon
|
samples
|
|
Hugo2016
|
PD1
|
Dataset 1
|
28
|
|
Prat2017
|
PD1
|
Dataset 2
|
25
|
|
Riaz2017
|
CTLA4
|
Dataset 3
|
56
|
|
TCGA
|
CTLA4
|
Dataset 4
|
19
|
|
VanAllen2015
|
CTLA4
|
Dataset 5
|
42
|
Scale data by dataset mean and standard deviation

Test gene list for differences in response
Longer list
Of 715 genes of interest, 551 are represented by gene symbol in the IMPRES set.
For each of those, compute ANOVA for linear model, with dataset and objective_response as effects.
Lowest p-values
|
|
P-value
|
|
CYFIP2
|
0.00389
|
|
CCR7
|
0.01251
|
|
NFKB2
|
0.01308
|
|
ST6GAL1
|
0.01470
|
|
CXCL13
|
0.01984
|
|
TNFRSF11B
|
0.02134
|
|
STAT3
|
0.02381
|
|
HSD11B1
|
0.02519
|
|
IL21R
|
0.03024
|
|
IL2RA
|
0.03321
|
|
CD3E
|
0.03585
|
|
SELE
|
0.03623
|
|
BCL6
|
0.03764
|
|
CARD11
|
0.04001
|
|
FLT3
|
0.04090
|
|
IL17RA
|
0.04130
|
|
IRF1
|
0.04222
|
|
NFKB1
|
0.04280
|
|
TLR8
|
0.04307
|
|
LTB
|
0.04324
|
Plots for top genes




















More focused list for SITC
Of 34 genes of interest, 27 are represented by gene symbol in the IMPRES set.
For each of those, compute ANOVA for linear model, with dataset and objective_response as effects.
P-values for the genes of interest
|
|
P-value
|
|
TIGIT
|
0.04394
|
|
CXCL9
|
0.05323
|
|
CXCR3
|
0.06164
|
|
PDCD1
|
0.06440
|
|
GZMB
|
0.06620
|
|
LAG3
|
0.06985
|
|
IDO1
|
0.07000
|
|
PRF1
|
0.07895
|
|
CD274
|
0.09495
|
|
CD8A
|
0.09949
|
|
IFNGR1
|
0.11839
|
|
TNFRSF9
|
0.12022
|
|
IRF8
|
0.13908
|
|
CXCL10
|
0.14721
|
|
THBD
|
0.16915
|
|
GZMA
|
0.18311
|
|
HAVCR2
|
0.20372
|
|
CCL5
|
0.23928
|
|
FLT3LG
|
0.32395
|
|
IFNGR2
|
0.34578
|
|
ITGAM
|
0.50607
|
|
XCL1
|
0.52420
|
|
BATF3
|
0.55156
|
|
NT5E
|
0.63707
|
|
ENTPD1
|
0.74859
|
|
TGFB1
|
0.78055
|
|
ITGAE
|
0.82085
|
Plots for each gene



























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